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Plot hierarchical clustering tree

Source: R/stat_hclust.R
plot.stat_hclust.Rd

Visualize hierarchical clustering with various tree layouts.

Usage

# S3 method for class 'stat_hclust'
plot(
  x,
  type = c("unrooted", "dendrogram", "fan", "phylogram"),
  color = NULL,
  tip_labels = NULL,
  ...
)

Arguments

x

A stat_hclust object

type

Character. Type of plot:

  • "unrooted": Unrooted phylogram (default, requires ape)

  • "dendrogram": Classic dendrogram

  • "fan": Fan/circular tree (requires ape)

  • "phylogram": Rectangular phylogram (requires ape)

color

Column name (bare or quoted) for coloring tips. If NULL and tree was cut, colors by cluster assignment.

tip_labels

Logical. Show tip labels? Default TRUE for small trees (<50 tips).

...

Additional arguments passed to plotting functions

Value

NULL (invisibly). Draws plot as side effect.

Details

Most plot types require the ape package. If not installed, falls back to base dendrogram plot.

Examples

if (FALSE) { # \dontrun{
hc <- boteft %>% stat_hclust(k = 4)

# Unrooted tree (default)
plot(hc)

# Color by original grouping
plot(hc, color = type)

# Color by clusters
plot(hc)  # Automatic if tree was cut

# Classic dendrogram
plot(hc, type = "dendrogram")

# Fan tree
plot(hc, type = "fan")
} # }